Hello Perdeep, Yes, you have understood the data correctly. If the cdsStart/cdsEnd are the same, then the transcript is defined as non-coding.
In some tracks the value will the same as the txStart (as in UCSC Genes) and in others it will the same as the txEnd (as in RefSeq Genes), but the interpretation is the same. Thanks Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/10/10 8:10 AM, Mehta, Perdeep wrote: > Hi, > > I am little confused with the data in knownGene in the Human section. As far > as I know, it has "Transcription start& end position" and "Coding region > start& end" information for an entry at column number 4, 5, 6, and 7 > respectively. > > Check out the following two entries, why does the Coding region start and end > (columns 6& 7) are identical, despite the fact that the uc002ybr just has > one exon (it could be a non-coding UTR) and the uc010gjw entry has 5 exons > (column 8). > > > [pme...@portal]$ grep "uc002ybr" knownGene.txt > uc002ybr.1 chr20 + 60513179 60515672 60513179 > 60513179 1 60513179, 60515672, uc002ybr.1 > > [pme...@portal]$ grep "uc010gjw" knownGene.txt > uc010gjw.1 chr20 + 58713536 59228976 58713536 > 58713536 5 58713536,58729462,58755892,58994077,59225766, > 58713700,58729557,58755971,58994213,59228976, uc010gjw.1 > > > I may be missing something. I will appreciate any help. > > Thanks, > perdeep > > Perdeep K. Mehta, PhD > Research Scientist, Bioinformatics > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > 262 Danny Thomas Place > Memphis, TN 38105-2794 > Tel: 901-595 3774 > http://www.hatwellcenter.org/ > > > Email Disclaimer: www.stjude.org/emaildisclaimer > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
